Job:PhD student in precision cancer bioinformatics | Charite, Berlin, Germany
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20 months ago

Ref. no.: BIH-42.21

The BIH Digital Health Center, headed by Prof. Roland Eils, develops and applies state-of-the-art and innovative technologies to healthcare research with a strong focus on machine learning, bioinformatics, imaging and genomics. The department has a strong standing within international consortium (e.g. Human Cell Atlas, ICGC, de.NBI, ELIXIR, EOSC), and have exceptional computational resources (in-house HPC, cloud, Nvidia DGX and FPGA technology).

We have recently established a precision medicine genomics platform, which aims to use whole genome and transcriptome sequencing for cancer patients. Building on top of an excellent existing pipeline, we aim to further develop the computational analytics part of the pipeline in the upcoming years. The position is based at the CCM campus in Berlin, Germany

Your area of responsibility:

  • Undertake and publish excellent scientific research
  • Interacting with other members of the clinical genomics program including management, pathology, genomics and clinical partners
  • Analyzing genome sequencing data for prospective patients, working closely with clinicians to identify actionable mutations
  • Analyzing genome sequencing data for retrospective studies
  • Development of new genomics workflows (e.g. supporting new genome references and genomics lesions such as STRs and enhancer hijacking) and interacting with our Data Management Platform team for deployment in a production environment
  • Development and implementation of novel computational methods that aid genomics based diagnostics and prognosis
  • Interacting with other collaborative sites, in particular the DKFZ and NCT in Heidelberg

Your profile:

  • A PhD candidate with a recent masters degree in bioinformatics, cancer genomics, computer science, medicine, physics or similar
  • Ambitious, self-driven, a thirst for answering scientific questions and aim to build a scientific career in biomedical data science research
  • Excellent programming proficiency especially in Python, R, Julia, bash or similar
  • Experience in designing and implementing data analysis pipelines
  • Experience with next generation sequencing data processing and analysis
  • Experience with linux based HPC or cloud environments
  • Fluent in English (written and spoken)

Qualifications – desirable:

  • Prior research experience in liquid biopsies, cancer genomics data, single cell ‘omics data, or spatial transcriptomics
  • Knowledge of transcriptional regulation and epigenomics
  • Knowledge of cancer immunology
  • Experience with machine learning methods (e. g. RF, NMF, VAE) and frameworks (e. g. PyTorch, TensorFlow, Keras, sklearn)
  • Experience with workflow management systems and similar paradigms (e. g. ELIXIR-WES, snakemake, NextFlow)

Start: Immediately

Length of employment: 3 years

Working time: 25,35 hrs./week

Pay scale: E13 acc. to collective agreement TVöD VKA – K

Contact person: For further information please contact Dr. Naveed Ishaque, E-Mail:

cancer ngs berlin clinical precision Job • 1.1k views

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